[Sparse] Add conversion between DGLGraph and SparseMatrix. (#5553)

benchmarks/benchmarks/api/bench_homograph_scipy_construction.py

@@ -15,12 +15,10 @@ from .. import utils
 @utils.parametrize("scipy_format", ["coo", "csr"])
 def track_time(size, scipy_format):
     matrix_dict = {
-        "small": dgl.data.CiteseerGraphDataset(verbose=False)[
-            0
-        ].adjacency_matrix(scipy_fmt=scipy_format),
-        "large": utils.get_livejournal().adjacency_matrix(
+        "small": dgl.data.CiteseerGraphDataset(verbose=False)[0].adj_external(
             scipy_fmt=scipy_format
         ),
+        "large": utils.get_livejournal().adj_external(scipy_fmt=scipy_format),
     }
 
     # dry run

docs/source/api/python/dgl.DGLGraph.rst

@@ -144,8 +144,9 @@ Methods for getting the adjacency and the incidence matrix of the graph.
     :toctree: ../../generated/
 
     DGLGraph.adj
-    DGLGraph.adj_sparse
     DGLGraph.adjacency_matrix
+    DGLGraph.adj_tensors
+    DGLGraph.adj_external
     DGLGraph.inc
     DGLGraph.incidence_matrix
 

examples/pytorch/TAHIN/data_loader.py

@@ -19,7 +19,7 @@ def split_data(hg, etype_name):
     pos_label = [1] * num_link
     pos_data = list(zip(user_item_src, user_item_dst, pos_label))
 
-    ui_adj = np.array(hg.adj(etype=etype_name).to_dense())
+    ui_adj = np.array(hg.adj_external(etype=etype_name).to_dense())
     full_idx = np.where(ui_adj == 0)
 
     sample = random.sample(range(0, len(full_idx[0])), num_link)

examples/pytorch/diffpool/model/dgl_layers/gnn.py

@@ -141,7 +141,7 @@ class DiffPoolBatchedGraphLayer(nn.Module):
         )  # size = (sum_N, batch_size * N_a)
 
         h = torch.matmul(torch.t(assign_tensor), feat)
-        adj = g.adjacency_matrix(transpose=True, ctx=device)
+        adj = g.adj_external(transpose=True, ctx=device)
         adj_new = torch.sparse.mm(adj, assign_tensor)
         adj_new = torch.mm(torch.t(assign_tensor), adj_new)
 

examples/pytorch/dtgrnn/dcrnn.py

@@ -71,7 +71,7 @@ class DiffConv(nn.Module):
 
     @staticmethod
     def get_weight_matrix(g):
-        adj = g.adj(scipy_fmt="coo")
+        adj = g.adj_external(scipy_fmt="coo")
         ind = g.in_degrees()
         outd = g.out_degrees()
         weight = g.edata["weight"]
@@ -81,7 +81,7 @@ class DiffConv(nn.Module):
     @staticmethod
     def diffuse(progress_g, weighted_adj, degree):
         device = progress_g.device
-        progress_adj = progress_g.adj(scipy_fmt="coo")
+        progress_adj = progress_g.adj_external(scipy_fmt="coo")
         progress_adj.data = progress_g.edata["weight"].cpu().numpy()
         ret_adj = sparse.coo_matrix(
             progress_adj @ (weighted_adj / degree.cpu().numpy())

examples/pytorch/ogb/ngnn_seal/main.py

@@ -85,7 +85,7 @@ class SEALOGBLDataset(Dataset):
 
         NIDs, EIDs = subg.ndata[dgl.NID], subg.edata[dgl.EID]
 
-        z = drnl_node_labeling(subg.adj(scipy_fmt="csr"), 0, 1)
+        z = drnl_node_labeling(subg.adj_external(scipy_fmt="csr"), 0, 1)
         edge_weights = (
             self.edge_weights[EIDs] if self.edge_weights is not None else None
         )

examples/pytorch/ogb/seal_ogbl/main.py

@@ -150,7 +150,7 @@ class SealSampler(Sampler):
             subg.remove_edges(edges_to_remove)
             # add double radius node labeling
             subg.ndata["z"] = self._double_radius_node_labeling(
-                subg.adj(scipy_fmt="csr")
+                subg.adj_external(scipy_fmt="csr")
             )
             subg_aug = subg.add_self_loop()
             if "weight" in subg.edata:

examples/pytorch/seal/utils.py

@@ -72,7 +72,7 @@ def drnl_node_labeling(subgraph, src, dst):
     Returns:
         z(Tensor): node labeling tensor
     """
-    adj = subgraph.adj().to_dense().numpy()
+    adj = subgraph.adj_external().to_dense().numpy()
     src, dst = (dst, src) if src > dst else (src, dst)
 
     idx = list(range(src)) + list(range(src + 1, adj.shape[0]))

examples/pytorch/vgae/train.py

@@ -125,7 +125,7 @@ def dgl_main():
     in_dim = feats.shape[-1]
 
     # generate input
-    adj_orig = graph.adjacency_matrix().to_dense()
+    adj_orig = graph.adj_external().to_dense()
 
     # build test set with 10% positive links
     (
@@ -142,7 +142,7 @@ def dgl_main():
     train_edge_idx = torch.tensor(train_edge_idx).to(device)
     train_graph = dgl.edge_subgraph(graph, train_edge_idx, relabel_nodes=False)
     train_graph = train_graph.to(device)
-    adj = train_graph.adjacency_matrix().to_dense().to(device)
+    adj = train_graph.adj_external().to_dense().to(device)
 
     # compute loss parameters
     weight_tensor, norm = compute_loss_para(adj)

python/dgl/heterograph.py

@@ -3754,14 +3754,90 @@ class DGLGraph(object):
         else:
             return deg
 
-    def adjacency_matrix(
-        self, transpose=False, ctx=F.cpu(), scipy_fmt=None, etype=None
-    ):
+    def adjacency_matrix(self, etype=None):
         """Alias of :meth:`adj`"""
-        return self.adj(transpose, ctx, scipy_fmt, etype)
+        return self.adj(etype)
+
+    def adj(self, etype=None, eweight_name=None):
+        """Get the adjacency matrix of the graph.
+
+        Parameters
+        ----------
+        etype : str or (str, str, str), optional
+            The type names of the edges. The allowed type name formats are:
+
+            * ``(str, str, str)`` for source node type, edge type and
+            destination node type.
+            * or one ``str`` edge type name if the name can uniquely identify a
+              triplet format in the graph.
+
+            Can be omitted if the graph has only one type of edges.
+
+        eweight_name : str, optional
+            The name of edge feature used as the non-zero values. If not given,
+            the non-zero values are all 1.
+
+        Returns
+        -------
+        SparseMatrix
+            The adjacency matrix.
+
+        Examples
+        --------
+
+        The following example uses PyTorch backend.
+
+        >>> import dgl
+        >>> import torch
+
+        >>> g = dgl.graph(([0, 1, 2], [1, 2, 3]))
+        >>> g.adj()
+        SparseMatrix(indices=tensor([[0, 1, 2],
+                                     [1, 2, 3]]),
+                     values=tensor([1., 1., 1.]),
+                     shape=(4, 4), nnz=3)
 
-    def adj(self, transpose=False, ctx=F.cpu(), scipy_fmt=None, etype=None):
-        """Return the adjacency matrix of edges of the given edge type.
+        >>> g = dgl.heterograph({
+        ...     ('user', 'follows', 'user'): ([0, 1], [0, 1]),
+        ...     ('developer', 'develops', 'game'): ([0, 1], [0, 2])
+        ... })
+
+        >>> g.adj(etype='develops')
+        SparseMatrix(indices=tensor([[0, 1],
+                                     [0, 2]]),
+                     values=tensor([1., 1.]),
+                     shape=(2, 3), nnz=2)
+        >>> g.edata['h'] = {('user', 'follows', 'user'): torch.tensor([3, 2])}
+        >>> g.adj(etype='follows', eweight_name='h')
+        SparseMatrix(indices=tensor([[0, 1],
+                                     [0, 1]]),
+                     values=tensor([3, 2]),
+                     shape=(2, 2), nnz=2)
+        """
+        assert F.backend_name == "pytorch", "Only PyTorch backend supports adj."
+        # Temporal fix to introduce a dependency on torch
+        import torch
+
+        from .sparse import spmatrix
+
+        etype = self.to_canonical_etype(etype)
+        indices = torch.stack(self.all_edges(etype=etype))
+        shape = (self.num_nodes(etype[0]), self.number_of_nodes(etype[2]))
+        if eweight_name is not None:
+            val = self.edata[eweight_name][etype]
+        else:
+            val = None
+        return spmatrix(
+            indices,
+            val=val,
+            shape=shape,
+        )
+
+    def adj_external(
+        self, transpose=False, ctx=F.cpu(), scipy_fmt=None, etype=None
+    ):
+        """Return the adjacency matrix in an external format, such as Scipy or
+        backend dependent sparse tensor.
 
         By default, a row of returned adjacency matrix represents the
         source of an edge and the column represents the destination.
@@ -3787,7 +3863,6 @@ class DGLGraph(object):
 
             Can be omitted if the graph has only one type of edges.
 
-
         Returns
         -------
         SparseTensor or scipy.sparse.spmatrix
@@ -3810,7 +3885,7 @@ class DGLGraph(object):
 
         Get a backend dependent sparse tensor. Here we use PyTorch for example.
 
-        >>> g.adj(etype='develops')
+        >>> g.adj_external(etype='develops')
         tensor(indices=tensor([[0, 1],
                                [0, 2]]),
                values=tensor([1., 1.]),
@@ -3818,7 +3893,7 @@ class DGLGraph(object):
 
         Get a scipy coo sparse matrix.
 
-        >>> g.adj(scipy_fmt='coo', etype='develops')
+        >>> g.adj_external(scipy_fmt='coo', etype='develops')
         <2x3 sparse matrix of type '<class 'numpy.int64'>'
            with 2 stored elements in COOrdinate format>
         """
@@ -3830,44 +3905,37 @@ class DGLGraph(object):
                 etid, transpose, scipy_fmt, False
             )
 
-    def adj_sparse(self, fmt, etype=None):
+    def adj_tensors(self, fmt, etype=None):
         """Return the adjacency matrix of edges of the given edge type as tensors of
         a sparse matrix representation.
-
         By default, a row of returned adjacency matrix represents the
         source of an edge and the column represents the destination.
-
         Parameters
         ----------
         fmt : str
             Either ``coo``, ``csr`` or ``csc``.
         etype : str or (str, str, str), optional
             The type names of the edges. The allowed type name formats are:
-
             * ``(str, str, str)`` for source node type, edge type and destination node type.
             * or one ``str`` edge type name if the name can uniquely identify a
               triplet format in the graph.
-
             Can be omitted if the graph has only one type of edges.
-
         Returns
         -------
         tuple[Tensor]
             If :attr:`fmt` is ``coo``, returns a pair of source and destination node ID
             tensors.
-
             If :attr:`fmt` is ``csr`` or ``csc``, return the CSR or CSC representation
             of the adjacency matrix as a triplet of tensors
             ``(indptr, indices, edge_ids)``.  Namely ``edge_ids`` could be an empty
             tensor with 0 elements, in which case the edge IDs are consecutive
             integers starting from 0.
-
         Examples
         --------
         >>> g = dgl.graph(([0, 1, 2], [1, 2, 3]))
-        >>> g.adj_sparse('coo')
+        >>> g.adj_tensors('coo')
         (tensor([0, 1, 2]), tensor([1, 2, 3]))
-        >>> g.adj_sparse('csr')
+        >>> g.adj_tensors('csr')
         (tensor([0, 1, 2, 3, 3]), tensor([1, 2, 3]), tensor([0, 1, 2]))
         """
         etid = self.get_etype_id(etype)

python/dgl/nn/pytorch/conv/cugraph_gatconv.py

@@ -163,7 +163,7 @@ class CuGraphGATConv(nn.Module):
             :math:`H` is the number of heads, and :math:`D_{out}` is size of
             output feature.
         """
-        offsets, indices, _ = g.adj_sparse("csc")
+        offsets, indices, _ = g.adj_tensors("csc")
 
         if g.is_block:
             if max_in_degree is None:

python/dgl/nn/pytorch/conv/cugraph_relgraphconv.py

@@ -177,7 +177,7 @@ class CuGraphRelGraphConv(nn.Module):
             New node features. Shape: :math:`(|V|, D_{out})`.
         """
         # Create csc-representation and cast etypes to int32.
-        offsets, indices, edge_ids = g.adj_sparse("csc")
+        offsets, indices, edge_ids = g.adj_tensors("csc")
         edge_types_perm = etypes[edge_ids.long()].int()
 
         # Create cugraph-ops graph.

python/dgl/nn/pytorch/conv/cugraph_sageconv.py

@@ -119,7 +119,7 @@ class CuGraphSAGEConv(nn.Module):
         torch.Tensor
             Output node features. Shape: :math:`(N, D_{out})`.
         """
-        offsets, indices, _ = g.adj_sparse("csc")
+        offsets, indices, _ = g.adj_tensors("csc")
 
         if g.is_block:
             if max_in_degree is None:

python/dgl/transforms/functional.py

@@ -1165,7 +1165,9 @@ def khop_adj(g, k):
             [0., 1., 3., 3., 1.]])
     """
     assert g.is_homogeneous, "only homogeneous graph is supported"
-    adj_k = g.adj(transpose=True, scipy_fmt=g.formats()["created"][0]) ** k
+    adj_k = (
+        g.adj_external(transpose=True, scipy_fmt=g.formats()["created"][0]) ** k
+    )
     return F.tensor(adj_k.todense().astype(np.float32))
 
 
@@ -1235,7 +1237,10 @@ def khop_graph(g, k, copy_ndata=True):
     """
     assert g.is_homogeneous, "only homogeneous graph is supported"
     n = g.num_nodes()
-    adj_k = g.adj(transpose=False, scipy_fmt=g.formats()["created"][0]) ** k
+    adj_k = (
+        g.adj_external(transpose=False, scipy_fmt=g.formats()["created"][0])
+        ** k
+    )
     adj_k = adj_k.tocoo()
     multiplicity = adj_k.data
     row = np.repeat(adj_k.row, multiplicity)
@@ -1447,7 +1452,7 @@ def laplacian_lambda_max(g):
     rst = []
     for g_i in g_arr:
         n = g_i.num_nodes()
-        adj = g_i.adj(
+        adj = g_i.adj_external(
             transpose=True, scipy_fmt=g_i.formats()["created"][0]
         ).astype(float)
         norm = sparse.diags(
@@ -1511,7 +1516,9 @@ def metapath_reachable_graph(g, metapath):
     """
     adj = 1
     for etype in metapath:
-        adj = adj * g.adj(etype=etype, scipy_fmt="csr", transpose=False)
+        adj = adj * g.adj_external(
+            etype=etype, scipy_fmt="csr", transpose=False
+        )
 
     adj = (adj != 0).tocsr()
     srctype = g.to_canonical_etype(metapath[0])[0]
@@ -2883,12 +2890,12 @@ def sort_csr_by_tag(g, tag, tag_offset_name="_TAG_OFFSET", tag_type="node"):
     >>> import torch
 
     >>> g = dgl.graph(([0,0,0,0,0,1,1,1],[0,1,2,3,4,0,1,2]))
-    >>> g.adjacency_matrix(scipy_fmt='csr').nonzero()
+    >>> g.adj_external(scipy_fmt='csr').nonzero()
     (array([0, 0, 0, 0, 0, 1, 1, 1], dtype=int32),
      array([0, 1, 2, 3, 4, 0, 1, 2], dtype=int32))
     >>> tag = torch.IntTensor([1,1,0,2,0])
     >>> g_sorted = dgl.sort_csr_by_tag(g, tag)
-    >>> g_sorted.adjacency_matrix(scipy_fmt='csr').nonzero()
+    >>> g_sorted.adj_external(scipy_fmt='csr').nonzero()
     (array([0, 0, 0, 0, 0, 1, 1, 1], dtype=int32),
      array([2, 4, 0, 1, 3, 2, 0, 1], dtype=int32))
     >>> g_sorted.ndata['_TAG_OFFSET']
@@ -2905,7 +2912,7 @@ def sort_csr_by_tag(g, tag, tag_offset_name="_TAG_OFFSET", tag_type="node"):
     (tensor([0, 0, 0, 0, 0, 1, 1, 1]), tensor([0, 1, 2, 3, 4, 0, 1, 2]))
     >>> tag = torch.tensor([1, 1, 0, 2, 0, 1, 1, 0])
     >>> g_sorted = dgl.sort_csr_by_tag(g, tag, tag_type='edge')
-    >>> g_sorted.adj(scipy_fmt='csr').nonzero()
+    >>> g_sorted.adj_external(scipy_fmt='csr').nonzero()
     (array([0, 0, 0, 0, 0, 1, 1, 1], dtype=int32), array([2, 4, 0, 1, 3, 2, 0, 1], dtype=int32))
     >>> g_sorted.srcdata['_TAG_OFFSET']
     tensor([[0, 2, 4, 5],
@@ -3011,12 +3018,12 @@ def sort_csc_by_tag(g, tag, tag_offset_name="_TAG_OFFSET", tag_type="node"):
     >>> import dgl
     >>> import torch
     >>> g = dgl.graph(([0,1,2,3,4,0,1,2],[0,0,0,0,0,1,1,1]))
-    >>> g.adjacency_matrix(scipy_fmt='csr', transpose=True).nonzero()
+    >>> g.adj_external(scipy_fmt='csr', transpose=True).nonzero()
     (array([0, 0, 0, 0, 0, 1, 1, 1], dtype=int32),
      array([0, 1, 2, 3, 4, 0, 1, 2], dtype=int32)))
     >>> tag = torch.IntTensor([1,1,0,2,0])
     >>> g_sorted = dgl.sort_csc_by_tag(g, tag)
-    >>> g_sorted.adjacency_matrix(scipy_fmt='csr', transpose=True).nonzero()
+    >>> g_sorted.adj_external(scipy_fmt='csr', transpose=True).nonzero()
     (array([0, 0, 0, 0, 0, 1, 1, 1], dtype=int32),
      array([2, 4, 0, 1, 3, 2, 0, 1], dtype=int32))
     >>> g_sorted.ndata['_TAG_OFFSET']
@@ -3031,7 +3038,7 @@ def sort_csc_by_tag(g, tag, tag_offset_name="_TAG_OFFSET", tag_type="node"):
     >>> g = dgl.graph(([0,1,2,3,4,0,1,2],[0,0,0,0,0,1,1,1]))
     >>> tag = torch.tensor([1, 1, 0, 2, 0, 1, 1, 0])
     >>> g_sorted = dgl.sort_csc_by_tag(g, tag, tag_type='edge')
-    >>> g_sorted.adj(scipy_fmt='csr', transpose=True).nonzero()
+    >>> g_sorted.adj_external(scipy_fmt='csr', transpose=True).nonzero()
     (array([0, 0, 0, 0, 0, 1, 1, 1], dtype=int32), array([2, 4, 0, 1, 3, 2, 0, 1], dtype=int32))
     >>> g_sorted.dstdata['_TAG_OFFSET']
     tensor([[0, 2, 4, 5],
@@ -3376,7 +3383,7 @@ def rcmk_perm(g):
     allowed_fmats = sum(g.formats().values(), [])
     if fmat not in allowed_fmats:
         g = g.formats(allowed_fmats + [fmat])
-    csr_adj = g.adj(scipy_fmt=fmat)
+    csr_adj = g.adj_external(scipy_fmt=fmat)
     perm = sparse.csgraph.reverse_cuthill_mckee(csr_adj)
     return perm.copy()
 
@@ -3573,7 +3580,7 @@ def random_walk_pe(g, k, eweight_name=None):
     """
     N = g.num_nodes()  # number of nodes
     M = g.num_edges()  # number of edges
-    A = g.adj(scipy_fmt="csr")  # adjacency matrix
+    A = g.adj_external(scipy_fmt="csr")  # adjacency matrix
     if eweight_name is not None:
         # add edge weights if required
         W = sparse.csr_matrix(
@@ -3657,7 +3664,7 @@ def lap_pe(g, k, padding=False, return_eigval=False):
         )
 
     # get laplacian matrix as I - D^-0.5 * A * D^-0.5
-    A = g.adj(scipy_fmt="csr")  # adjacency matrix
+    A = g.adj_external(scipy_fmt="csr")  # adjacency matrix
     N = sparse.diags(
         F.asnumpy(g.in_degrees()).clip(1) ** -0.5, dtype=float
     )  # D^-1/2
@@ -3789,7 +3796,7 @@ def double_radius_node_labeling(g, src, dst):
     >>> dgl.double_radius_node_labeling(g, 0, 1)
     tensor([1, 1, 3, 2, 3, 7, 0])
     """
-    adj = g.adj(scipy_fmt="csr")
+    adj = g.adj_external(scipy_fmt="csr")
     src, dst = (dst, src) if src > dst else (src, dst)
 
     idx = list(range(src)) + list(range(src + 1, adj.shape[0]))
@@ -3899,14 +3906,14 @@ def shortest_dist(g, root=None, return_paths=False):
     """
     if root is None:
         dist, pred = sparse.csgraph.shortest_path(
-            g.adj(scipy_fmt="csr"),
+            g.adj_external(scipy_fmt="csr"),
             return_predecessors=True,
             unweighted=True,
             directed=True,
         )
     else:
         dist, pred = sparse.csgraph.dijkstra(
-            g.adj(scipy_fmt="csr"),
+            g.adj_external(scipy_fmt="csr"),
             directed=True,
             indices=root,
             return_predecessors=True,
@@ -4010,7 +4017,7 @@ def svd_pe(g, k, padding=False, random_flip=True):
             "The number of singular values k must be no greater than the "
             "number of nodes n, but " + f"got {k} and {n} respectively."
         )
-    a = g.adj(ctx=g.device, scipy_fmt="coo").toarray()
+    a = g.adj_external(ctx=g.device, scipy_fmt="coo").toarray()
     u, d, vh = scipy.linalg.svd(a)
     v = vh.transpose()
     m = min(n, k)

tests/python/common/test_heterograph-misc.py

@@ -144,11 +144,11 @@ def test_query():
         assert F.allclose(g.out_degrees([8, 9]), F.tensor([0, 1]))
 
         assert np.array_equal(
-            F.sparse_to_numpy(g.adjacency_matrix(transpose=True)),
+            F.sparse_to_numpy(g.adj_external(transpose=True)),
             scipy_coo_input().toarray().T,
         )
         assert np.array_equal(
-            F.sparse_to_numpy(g.adjacency_matrix(transpose=False)),
+            F.sparse_to_numpy(g.adj_external(transpose=False)),
             scipy_coo_input().toarray(),
         )
 
@@ -245,11 +245,11 @@ def test_query():
         assert F.allclose(g.out_degrees([8, 9]), F.tensor([0, 1]))
 
         assert np.array_equal(
-            F.sparse_to_numpy(g.adjacency_matrix(transpose=True)),
+            F.sparse_to_numpy(g.adj_external(transpose=True)),
             scipy_coo_input().toarray().T,
         )
         assert np.array_equal(
-            F.sparse_to_numpy(g.adjacency_matrix(transpose=False)),
+            F.sparse_to_numpy(g.adj_external(transpose=False)),
             scipy_coo_input().toarray(),
         )
 
@@ -308,12 +308,12 @@ def test_scipy_adjmat():
     g.add_nodes(10)
     g.add_edges(range(9), range(1, 10))
 
-    adj_0 = g.adj(scipy_fmt="csr")
-    adj_1 = g.adj(scipy_fmt="coo")
+    adj_0 = g.adj_external(scipy_fmt="csr")
+    adj_1 = g.adj_external(scipy_fmt="coo")
     assert np.array_equal(adj_0.toarray(), adj_1.toarray())
 
-    adj_t0 = g.adj(transpose=False, scipy_fmt="csr")
-    adj_t_1 = g.adj(transpose=False, scipy_fmt="coo")
+    adj_t0 = g.adj_external(transpose=False, scipy_fmt="csr")
+    adj_t_1 = g.adj_external(transpose=False, scipy_fmt="coo")
     assert np.array_equal(adj_0.toarray(), adj_1.toarray())
 
 

tests/python/common/test_heterograph.py

@@ -708,41 +708,57 @@ def _test_edge_ids():
     assert eid == 0
 
 
+@pytest.mark.skipif(
+    F.backend_name != "pytorch", reason="Only support PyTorch for now"
+)
 @parametrize_idtype
 def test_adj(idtype):
     g = create_test_heterograph(idtype)
-    adj = F.sparse_to_numpy(g.adj(transpose=True, etype="follows"))
+    adj = g.adj("follows")
+    assert F.asnumpy(adj.indices()).tolist() == [[0, 1], [1, 2]]
+    assert np.allclose(F.asnumpy(adj.val), np.array([1, 1]))
+    g.edata["h"] = {("user", "plays", "game"): F.tensor([1, 2, 3, 4])}
+    print(g.edata["h"])
+    adj = g.adj("plays", "h")
+    assert F.asnumpy(adj.indices()).tolist() == [[0, 1, 2, 1], [0, 0, 1, 1]]
+    assert np.allclose(F.asnumpy(adj.val), np.array([1, 2, 3, 4]))
+
+
+@parametrize_idtype
+def test_adj_external(idtype):
+    g = create_test_heterograph(idtype)
+    adj = F.sparse_to_numpy(g.adj_external(transpose=True, etype="follows"))
     assert np.allclose(
         adj, np.array([[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [0.0, 1.0, 0.0]])
     )
-    adj = F.sparse_to_numpy(g.adj(transpose=False, etype="follows"))
+    adj = F.sparse_to_numpy(g.adj_external(transpose=False, etype="follows"))
     assert np.allclose(
         adj, np.array([[0.0, 1.0, 0.0], [0.0, 0.0, 1.0], [0.0, 0.0, 0.0]])
     )
-    adj = F.sparse_to_numpy(g.adj(transpose=True, etype="plays"))
+    adj = F.sparse_to_numpy(g.adj_external(transpose=True, etype="plays"))
     assert np.allclose(adj, np.array([[1.0, 1.0, 0.0], [0.0, 1.0, 1.0]]))
-    adj = F.sparse_to_numpy(g.adj(transpose=False, etype="plays"))
+    adj = F.sparse_to_numpy(g.adj_external(transpose=False, etype="plays"))
     assert np.allclose(adj, np.array([[1.0, 0.0], [1.0, 1.0], [0.0, 1.0]]))
 
-    adj = g.adj(transpose=True, scipy_fmt="csr", etype="follows")
+    adj = g.adj_external(transpose=True, scipy_fmt="csr", etype="follows")
     assert np.allclose(
         adj.todense(),
         np.array([[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [0.0, 1.0, 0.0]]),
     )
-    adj = g.adj(transpose=True, scipy_fmt="coo", etype="follows")
+    adj = g.adj_external(transpose=True, scipy_fmt="coo", etype="follows")
     assert np.allclose(
         adj.todense(),
         np.array([[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [0.0, 1.0, 0.0]]),
     )
-    adj = g.adj(transpose=True, scipy_fmt="csr", etype="plays")
+    adj = g.adj_external(transpose=True, scipy_fmt="csr", etype="plays")
     assert np.allclose(
         adj.todense(), np.array([[1.0, 1.0, 0.0], [0.0, 1.0, 1.0]])
     )
-    adj = g.adj(transpose=True, scipy_fmt="coo", etype="plays")
+    adj = g.adj_external(transpose=True, scipy_fmt="coo", etype="plays")
     assert np.allclose(
         adj.todense(), np.array([[1.0, 1.0, 0.0], [0.0, 1.0, 1.0]])
     )
-    adj = F.sparse_to_numpy(g["follows"].adj(transpose=True))
+    adj = F.sparse_to_numpy(g["follows"].adj_external(transpose=True))
     assert np.allclose(
         adj, np.array([[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [0.0, 1.0, 0.0]])
     )
@@ -3535,7 +3551,7 @@ def test_create_block(idtype):
 
 @parametrize_idtype
 @pytest.mark.parametrize("fmt", ["coo", "csr", "csc"])
-def test_adj_sparse(idtype, fmt):
+def test_adj_tensors(idtype, fmt):
     if fmt == "coo":
         A = ssp.random(10, 10, 0.2).tocoo()
         A.data = np.arange(20)
@@ -3562,11 +3578,11 @@ def test_adj_sparse(idtype, fmt):
     A_coo = A.tocoo()
     A_csr = A.tocsr()
     A_csc = A.tocsc()
-    row, col = g.adj_sparse("coo")
+    row, col = g.adj_tensors("coo")
     assert np.array_equal(F.asnumpy(row), A_coo.row)
     assert np.array_equal(F.asnumpy(col), A_coo.col)
 
-    indptr, indices, eids = g.adj_sparse("csr")
+    indptr, indices, eids = g.adj_tensors("csr")
     assert np.array_equal(F.asnumpy(indptr), A_csr.indptr)
     if fmt == "csr":
         assert len(eids) == 0
@@ -3578,7 +3594,7 @@ def test_adj_sparse(idtype, fmt):
         indices_sorted_np[A_csr.data] = A_csr.indices
         assert np.array_equal(F.asnumpy(indices_sorted), indices_sorted_np)
 
-    indptr, indices, eids = g.adj_sparse("csc")
+    indptr, indices, eids = g.adj_tensors("csc")
     assert np.array_equal(F.asnumpy(indptr), A_csc.indptr)
     if fmt == "csc":
         assert len(eids) == 0

tests/python/common/test_traversal.py

@@ -70,7 +70,7 @@ def test_topological_nodes(idtype, n=100):
 
     layers_dgl = dgl.topological_nodes_generator(g)
 
-    adjmat = g.adjacency_matrix(transpose=True)
+    adjmat = g.adj_external(transpose=True)
 
     def tensor_topo_traverse():
         n = g.num_nodes()

tests/python/common/transforms/test_functional-sort.py

@@ -74,8 +74,8 @@ def test_sort_with_tag(idtype):
         new_g = dgl.sort_csr_by_tag(
             g, tag if tag_type == "node" else edge_tag_dst, tag_type=tag_type
         )
-        old_csr = g.adjacency_matrix(scipy_fmt="csr")
-        new_csr = new_g.adjacency_matrix(scipy_fmt="csr")
+        old_csr = g.adj_external(scipy_fmt="csr")
+        new_csr = new_g.adj_external(scipy_fmt="csr")
         assert check_sort(new_csr, tag, new_g.dstdata["_TAG_OFFSET"])
         assert not check_sort(
             old_csr, tag
@@ -85,8 +85,8 @@ def test_sort_with_tag(idtype):
         new_g = dgl.sort_csc_by_tag(
             g, tag if tag_type == "node" else edge_tag_src, tag_type=tag_type
         )
-        old_csc = g.adjacency_matrix(transpose=True, scipy_fmt="csr")
-        new_csc = new_g.adjacency_matrix(transpose=True, scipy_fmt="csr")
+        old_csc = g.adj_external(transpose=True, scipy_fmt="csr")
+        new_csc = new_g.adj_external(transpose=True, scipy_fmt="csr")
         assert check_sort(new_csc, tag, new_g.srcdata["_TAG_OFFSET"])
         assert not check_sort(old_csc, tag)
 
@@ -103,14 +103,14 @@ def test_sort_with_tag_bipartite(idtype):
     vtag = F.tensor(np.random.choice(num_tags, g.num_nodes("_V")))
 
     new_g = dgl.sort_csr_by_tag(g, vtag)
-    old_csr = g.adjacency_matrix(scipy_fmt="csr")
-    new_csr = new_g.adjacency_matrix(scipy_fmt="csr")
+    old_csr = g.adj_external(scipy_fmt="csr")
+    new_csr = new_g.adj_external(scipy_fmt="csr")
     assert check_sort(new_csr, vtag, new_g.nodes["_U"].data["_TAG_OFFSET"])
     assert not check_sort(old_csr, vtag)
 
     new_g = dgl.sort_csc_by_tag(g, utag)
-    old_csc = g.adjacency_matrix(transpose=True, scipy_fmt="csr")
-    new_csc = new_g.adjacency_matrix(transpose=True, scipy_fmt="csr")
+    old_csc = g.adj_external(transpose=True, scipy_fmt="csr")
+    new_csc = new_g.adj_external(transpose=True, scipy_fmt="csr")
     assert check_sort(new_csc, utag, new_g.nodes["_V"].data["_TAG_OFFSET"])
     assert not check_sort(old_csc, utag)
 

tests/python/common/transforms/test_transform.py

@@ -3135,10 +3135,12 @@ def test_module_sign(g):
 
     ctx = F.ctx()
     g = g.to(ctx)
-    adj = g.adj(transpose=True, scipy_fmt="coo").todense()
+    adj = g.adj_external(transpose=True, scipy_fmt="coo").todense()
     adj = torch.tensor(adj).float().to(ctx)
 
-    weight_adj = g.adj(transpose=True, scipy_fmt="coo").astype(float).todense()
+    weight_adj = (
+        g.adj_external(transpose=True, scipy_fmt="coo").astype(float).todense()
+    )
     weight_adj = torch.tensor(weight_adj).float().to(ctx)
     src, dst = g.edges()
     src, dst = src.long(), dst.long()

tests/python/mxnet/test_nn.py

@@ -34,7 +34,7 @@ def test_graph_conv(idtype, out_dim):
     g = dgl.from_networkx(nx.path_graph(3))
     g = g.astype(idtype).to(F.ctx())
     ctx = F.ctx()
-    adj = g.adjacency_matrix(transpose=True, ctx=ctx)
+    adj = g.adj_external(transpose=True, ctx=ctx)
 
     conv = nn.GraphConv(5, out_dim, norm="none", bias=True)
     conv.initialize(ctx=ctx)
@@ -154,7 +154,7 @@ def _S2AXWb(A, N, X, W, b):
 def test_tagconv(out_dim):
     g = dgl.from_networkx(nx.path_graph(3)).to(F.ctx())
     ctx = F.ctx()
-    adj = g.adjacency_matrix(transpose=True, ctx=ctx)
+    adj = g.adj_external(transpose=True, ctx=ctx)
     norm = mx.nd.power(g.in_degrees().astype("float32"), -0.5)
 
     conv = nn.TAGConv(5, out_dim, bias=True)
@@ -361,7 +361,7 @@ def test_dense_cheb_conv(out_dim):
     for k in range(1, 4):
         ctx = F.ctx()
         g = dgl.from_scipy(sp.sparse.random(100, 100, density=0.3)).to(F.ctx())
-        adj = g.adjacency_matrix(transpose=True, ctx=ctx).tostype("default")
+        adj = g.adj_external(transpose=True, ctx=ctx).tostype("default")
         cheb = nn.ChebConv(5, out_dim, k)
         dense_cheb = nn.DenseChebConv(5, out_dim, k)
         cheb.initialize(ctx=ctx)
@@ -387,7 +387,7 @@ def test_dense_cheb_conv(out_dim):
 def test_dense_graph_conv(idtype, g, norm_type, out_dim):
     g = g.astype(idtype).to(F.ctx())
     ctx = F.ctx()
-    adj = g.adjacency_matrix(transpose=True, ctx=ctx).tostype("default")
+    adj = g.adj_external(transpose=True, ctx=ctx).tostype("default")
     conv = nn.GraphConv(5, out_dim, norm=norm_type, bias=True)
     dense_conv = nn.DenseGraphConv(5, out_dim, norm=norm_type, bias=True)
     conv.initialize(ctx=ctx)
@@ -408,7 +408,7 @@ def test_dense_graph_conv(idtype, g, norm_type, out_dim):
 def test_dense_sage_conv(idtype, g, out_dim):
     g = g.astype(idtype).to(F.ctx())
     ctx = F.ctx()
-    adj = g.adjacency_matrix(transpose=True, ctx=ctx).tostype("default")
+    adj = g.adj_external(transpose=True, ctx=ctx).tostype("default")
     sage = nn.SAGEConv(5, out_dim, "gcn")
     dense_sage = nn.DenseSAGEConv(5, out_dim)
     sage.initialize(ctx=ctx)